bio-biosql 0.0.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 6b56ab2936a2ea661de08ec2fa82104a41c25208
+  data.tar.gz: d9f69c1c27b3c4d1d7a82dd346cf534226c1fda7
+SHA512:
+  metadata.gz: 133e9c0940a2443a219eff533dd0ffbf38d929a6f4049ef79e3799ac0789cd5d19121d9c011ceaa236f0d2a04fc833dc2c49506e938402b16dcca0ff1397894e
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/rdoc/
+/pkg/
+/spec/reports/
+/tmp/
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>bioruby</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.rubypeople.rdt.core.rubybuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.rubypeople.rdt.core.rubynature</nature>
+	</natures>
+</projectDescription>

data/BSDL

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+Copyright (C) 1993-2013 Yukihiro Matsumoto. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.

data/COPYING

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+bio-biosql is copyrighted free software by BioRuby project <staff@bioruby.org>.
+You can redistribute it and/or modify it under either the terms of the
+2-clause BSDL (see the file BSDL), or the conditions below:
+
+  1. You may make and give away verbatim copies of the source form of the
+     software without restriction, provided that you duplicate all of the
+     original copyright notices and associated disclaimers.
+
+  2. You may modify your copy of the software in any way, provided that
+     you do at least ONE of the following:
+
+       a) place your modifications in the Public Domain or otherwise
+          make them Freely Available, such as by posting said
+	  modifications to Usenet or an equivalent medium, or by allowing
+	  the author to include your modifications in the software.
+
+       b) use the modified software only within your corporation or
+          organization.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  3. You may distribute the software in object code or binary form,
+     provided that you do at least ONE of the following:
+
+       a) distribute the binaries and library files of the software,
+	  together with instructions (in the manual page or equivalent)
+	  on where to get the original distribution.
+
+       b) accompany the distribution with the machine-readable source of
+	  the software.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  4. You may modify and include the part of the software into any other
+     software (possibly commercial).  But some files in the distribution
+     are not written by the author, so that they are not under these terms.
+
+     For the list of those files and their copying conditions, see the
+     file LEGAL.
+
+  5. The scripts and library files supplied as input to or produced as 
+     output from the software do not automatically fall under the
+     copyright of the software, but belong to whomever generated them, 
+     and may be sold commercially, and may be aggregated with this
+     software.
+
+  6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+     IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+     PURPOSE.

data/COPYING.ja

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+本プログラムはフリーソフトウェアです．2-clause BSDL
+または以下に示す条件で本プログラムを再配布できます
+2-clause BSDLについてはBSDLファイルを参照して下さい．
+
+  1. 複製は制限なく自由です．
+
+  2. 以下の条件のいずれかを満たす時に本プログラムのソースを
+     自由に変更できます．
+
+     (a) ネットニューズにポストしたり，作者に変更を送付する
+         などの方法で，変更を公開する．
+
+     (b) 変更した本プログラムを自分の所属する組織内部だけで
+         使う．
+
+     (c) 変更点を明示したうえ，ソフトウェアの名前を変更する．
+         そのソフトウェアを配布する時には変更前の本プログラ
+         ムも同時に配布する．または変更前の本プログラムのソー
+         スの入手法を明示する．
+
+     (d) その他の変更条件を作者と合意する．
+
+  3. 以下の条件のいずれかを満たす時に本プログラムをコンパイ
+     ルしたオブジェクトコードや実行形式でも配布できます．
+
+     (a) バイナリを受け取った人がソースを入手できるように，
+         ソースの入手法を明示する．
+
+     (b) 機械可読なソースコードを添付する．
+
+     (c) 変更を行ったバイナリは名前を変更したうえ，オリジナ
+         ルのソースコードの入手法を明示する．
+
+     (d) その他の配布条件を作者と合意する．
+
+  4. 他のプログラムへの引用はいかなる目的であれ自由です．た
+     だし，本プログラムに含まれる他の作者によるコードは，そ
+     れぞれの作者の意向による制限が加えられる場合があります．
+
+     それらファイルの一覧とそれぞれの配布条件などに付いては
+     LEGALファイルを参照してください．
+
+  5. 本プログラムへの入力となるスクリプトおよび，本プログラ
+     ムからの出力の権利は本プログラムの作者ではなく，それぞ
+     れの入出力を生成した人に属します．また，本プログラムに
+     組み込まれるための拡張ライブラリについても同様です．
+
+  6. 本プログラムは無保証です．作者は本プログラムをサポート
+     する意志はありますが，プログラム自身のバグあるいは本プ
+     ログラムの実行などから発生するいかなる損害に対しても責
+     任を持ちません．

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in bio-biosql.gemspec
+gemspec

data/LEGAL

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+LEGAL NOTICE INFORMATION
+------------------------
+
+All the files in this distribution are covered under either the Ruby's
+license (see the file COPYING) or public-domain except some files
+mentioned below.
+
+
+(no files)

data/README.md

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+# Bio::SQL -- BioRuby BioSQL Plugin
+
+IMPORTANT NOTICE: This package is preliminary experimental state.
+It may not work as expected.
+Please fix bugs and report to us.
+
+bio-biosql is a [BioSQL](http://biosql.org/) plugin for
+[BioRuby](http://bioruby.org/), an open source bioinformatics
+library for Ruby.
+
+BioSQL is a set of SQL schema for storing biological sequences
+with meta-data. BioSQL supports major open-source database engines.
+See [BioSQL Documentation](http://biosql.org/) for details.
+
+This code written in Ruby has historically been part of the core BioRuby
+[gem](https://github.com/bioruby/bioruby), but has been split into its
+own gem as part of an effort to
+[modularize](http://bioruby.open-bio.org/wiki/Plugins)
+BioRuby. bio-biosql and many more plugins are available at
+[biogems.info](http://www.biogems.info/).
+
+This code was initially written by Toshiaki Katayama.
+Raoul Jean Pierre Bonnal greatly improved the code with introducing
+ActiveRecord. For details of development, see
+[github.com/helios/bioruby](https://github.com/helios/bioruby),
+[github.com/bioruby/bioruby](https://github.com/bioruby/bioruby),
+and the BioRuby mailing list archives.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'bio-biosql'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install bio-biosql
+
+## Requirements
+
+In addition to the dependency written in Gemfile,
+at least one ActiveRecord adapter will be needed.
+
+* [pg](http://rubygems.org/gems/pg)
+* [sqlite-ruby](http://rubygems.org/gems/sqlite-ruby)
+* [sqlite3](http://rubygems.org/gems/sqlite3)
+* [mysql](http://rubygems.org/gems/mysql)
+* [mysql2](http://rubygems.org/gems/mysql2)
+* [activerecord-oracle_enhanced-adapter](http://rubygems.org/gems/activerecord-oracle_enhanced-adapter)
+
+TODO: Please test Bio::SQL with above adapters.
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it ( https://github.com/bioruby/bioruby-biosql/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+require 'rdoc/task'
+require 'rake/testtask'
+
+task :default => "test"
+
+Rake::TestTask.new do |t|
+  t.test_files = FileList["test/unit/**/test_*.rb"]
+end
+
+Rake::RDocTask.new do |r|
+  r.rdoc_dir = "rdoc"
+  r.rdoc_files.include("README.md",
+                       "COPYING", "COPYING.ja", "BSDL", 
+                       "lib/**/*.rb")
+  r.main = "README.md"
+  r.options << '--title' << 'Bio::SQL API documentation'
+  r.options << '--line-numbers'
+end

data/bio-biosql.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'bio-biosql/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "bio-biosql"
+  spec.version       = Bio::SQL::VERSION
+  spec.authors       = ["BioRuby project"]
+  spec.email         = ["staff@bioruby.org"]
+  spec.summary       = %q{BioSQL plugin for BioRuby}
+  spec.description   = %q{Provides BioSQL support for BioRuby.}
+  spec.homepage      = "http://github.com/bioruby/bioruby-biosql"
+  spec.license       = "Ruby"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.extra_rdoc_files = [ "README.md",
+                            "COPYING", "COPYING.ja", "BSDL"
+                          ]
+  spec.rdoc_options << '--main' << 'README.md'
+  spec.rdoc_options << '--title' << 'Bio::SQL API documentation'
+  spec.rdoc_options << '--line-numbers'
+
+  spec.add_runtime_dependency "bio", "~> 1.5.0"
+  spec.add_runtime_dependency "activerecord", "~> 3.0.10"
+  spec.add_runtime_dependency "composite_primary_keys", "~> 3.1.10"
+
+  spec.add_development_dependency "bundler", "~> 1.7"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rdoc", "~> 4"
+  spec.add_development_dependency "test-unit", "~> 3"
+end

data/lib/bio-biosql/version.rb

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+module Bio
+  module SQL
+    VERSION = "0.0.0"
+  end
+end

data/lib/bio/db/biosql/biosql_to_biosequence.rb

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+#
+# = bio/db/biosql/biosql_to_biosequence.rb - Bio::SQL::Sequence to Bio::Sequence adapter module
+#
+# Copyright::   Copyright (C) 2008
+#               Naohisa Goto <ng@bioruby.org>,
+#               Raoul Jean Pierre Bonnal
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+require 'bio/sequence'
+require 'bio/sequence/adapter'
+require 'bio/sequence/dblink'
+
+# Internal use only. Normal users should not use this module.
+#
+# Bio::SQL::Sequence to Bio::Sequence adapter module.
+# It is internally used in Bio::SQL::Sequence#to_biosequence.
+#
+module Bio::Sequence::Adapter::BioSQL
+
+  extend Bio::Sequence::Adapter
+
+  private
+
+  def_biosequence_adapter :seq 
+  
+  def_biosequence_adapter :entry_id
+
+  def_biosequence_adapter :primary_accession
+
+  def_biosequence_adapter :secondary_accessions
+
+  def_biosequence_adapter :molecule_type
+
+  #--
+  #TODO: identify where is stored data_class in biosql      
+  #++
+
+  def_biosequence_adapter :data_class
+
+  def_biosequence_adapter :definition, :description
+
+  def_biosequence_adapter :topology
+
+  def_biosequence_adapter :date_created
+
+  def_biosequence_adapter :date_modified
+  #do |bs|
+   #   Date.parse(bs.date_modified.to_s).strftime("%d-%b-%Y").upcase
+    # end
+
+  def_biosequence_adapter :division
+
+  def_biosequence_adapter :sequence_version
+
+  def_biosequence_adapter :keywords
+
+  def_biosequence_adapter :species
+
+  def_biosequence_adapter :classification, :taxonomy
+
+  def_biosequence_adapter :references
+
+  def_biosequence_adapter :features
+  
+  def_biosequence_adapter :comments
+
+  def_biosequence_adapter :other_seqids do |orig|
+    orig.identifier.split(',').collect do |dblink|
+      database, id = dblink.split(':')
+      Bio::Sequence::DBLink.new(database,id)
+    end
+  end
+
+end #module Bio::Sequence::Adapter::BioSQL
+

data/lib/bio/db/biosql/sequence.rb

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+
+#TODO save on db reading from a genbank or embl object
+module Bio
+  class SQL
+
+
+
+    class Sequence
+      private
+      #      example
+      #      bioentry_qualifier_anchor :molecule_type, :synonym=>'mol_type'
+      #      this function creates other 3 functions, molecule_type, molecule_type=, molecule_type_update
+      #molecule_type => return an array of strings, where each string is the value associated with the qualifier, ordered by rank.
+      #molecule_type=value add a bioentry_qualifier value to the table
+      #molecule_type_update(value, rank) update an entry of the table with an existing rank
+      #the method inferr the qualifier term from the name of the first symbol, or you can specify a synonym to use
+
+      #creating an object with to_biosql is transaction safe.
+
+      #TODO: implement setting for more than a qualifier-vale.
+      def self.bioentry_qualifier_anchor(sym, *args)
+        options = args.first || Hash.new
+        #options.assert_valid_keys(:rank,:synonym,:multi)
+        method_reader = sym.to_s.to_sym
+        method_writer_operator = (sym.to_s+"=").to_sym
+        method_writer_modder = (sym.to_s+"_update").to_sym
+        synonym = options[:synonym].nil? ? sym.to_s : options[:synonym]
+
+        #DELETE        #Bio::SQL::Term.create(:name=>synonym, :ontology=> Bio::SQL::Ontology.find_by_name('Annotation Tags')) unless Bio::SQL::Term.exists?(:name =>synonym)
+        send :define_method, method_reader do
+          #return an array of bioentry_qualifier_values
+          begin
+            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
+            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
+            bioentry_qualifier_values = @entry.bioentry_qualifier_values.all(:conditions=>["term_id = ?",term.term_id])
+            data = bioentry_qualifier_values.map{|row| row.value} unless bioentry_qualifier_values.nil?
+            begin
+              # this block try to check if the data retrived is a
+              # Date or not and change it according to GenBank/EMBL format
+              # in that case return a string
+              # otherwise the []
+              Date.parse(data.to_s).strftime("%d-%b-%Y").upcase
+            rescue ArgumentError, TypeError, NoMethodError, NameError
+              data
+            end
+          rescue Exception => e
+            puts "Reader Error: #{synonym} #{e.message}"
+          end
+        end
+
+        send :define_method, method_writer_operator do |value|
+          begin
+            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
+            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
+            datas = @entry.bioentry_qualifier_values.all(:conditions=>["term_id = ?",term.term_id])
+            #add an element incrementing the rank or setting the first to 1
+            be_qu_va=@entry.bioentry_qualifier_values.build({:term=>term, :rank=>(datas.empty? ? 1 : datas.last.rank.succ), :value=>value})
+            be_qu_va.save
+          rescue Exception => e
+            puts "WriterOperator= Error: #{synonym} #{e.message}"
+          end
+        end
+
+        send :define_method, method_writer_modder do |value, rank|
+          begin
+            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
+            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
+            data = @entry.bioentry_qualifier_values.all(:term_id=>term.term_id, :rank=>rank)
+            if data.nil?
+              send method_writer_operator, value
+            else
+              data.value=value
+              data.save
+            end
+          rescue Exception => e
+            puts "WriterModder Error: #{synonym} #{e.message}"
+          end
+        end
+
+      end
+
+      public
+      attr_reader :entry
+
+      def delete
+        #TODO: check is references connected to this bioentry are leaf or not.
+        #actually I think it should be more sofisticated, check if there are
+        #other bioentries connected to references; if not delete 'em
+        @entry.references.each { |ref| ref.delete if ref.bioentries.size==1}
+        @entry.destroy
+      end
+
+      def get_seqfeature(sf)
+
+        #in seqfeature BioSQL class
+        locations_str = sf.locations.map{|loc| loc.to_s}.join(',')
+        #pp sf.locations.inspect
+        locations_str = "join(#{locations_str})" if sf.locations.count>1
+        Bio::Feature.new(sf.type_term.name, locations_str,sf.seqfeature_qualifier_values.collect{|sfqv| Bio::Feature::Qualifier.new(sfqv.term.name,sfqv.value)})
+      end
+
+      def length=(len)
+        @entry.biosequence.length=len
+      end
+
+      def initialize(options={})
+        #options.assert_valid_keys(:entry, :biodatabase,:biosequence)
+        return @entry = options[:entry] unless options[:entry].nil?
+
+        return to_biosql(options[:biosequence], options[:biodatabase]) unless options[:biosequence].nil? or options[:biodatabase].nil?
+
+      end
+
+      def to_biosql(bs,biodatabase)
+        #DELETE        #Transcaction works greatly!!!
+        begin
+          #DELETE          Bioentry.transaction do
+          @entry = biodatabase.bioentries.build({:name=>bs.entry_id})
+
+          puts "primary" if $DEBUG
+          self.primary_accession = bs.primary_accession
+
+          puts "def" if $DEBUG
+          self.definition = bs.definition unless bs.definition.nil?
+
+          puts "seqver" if $DEBUG
+          self.sequence_version = bs.sequence_version || 0
+
+          puts "divi" if $DEBUG
+          self.division = bs.division unless bs.division.nil?
+
+          puts "identifier" if $DEBUG
+          self.identifier = bs.other_seqids.collect{|dblink| "#{dblink.database}:#{dblink.id}"}.join(';') unless bs.other_seqids.nil?
+          @entry.save
+          puts "secacc" if $DEBUG
+
+          bs.secondary_accessions.each do |sa|
+            puts "#{sa}" if $DEBUG
+            #write as qualifier every secondary accession into the array
+            self.secondary_accessions = sa
+          end unless bs.secondary_accessions.nil?
+
+
+          #to create the sequence entry needs to exists
+          puts "seq" if $DEBUG
+          puts bs.seq if $DEBUG
+          self.seq = bs.seq unless bs.seq.nil?
+          puts "mol" if $DEBUG
+
+          self.molecule_type = bs.molecule_type unless bs.molecule_type.nil?
+          puts "dc" if $DEBUG
+
+          self.data_class = bs.data_class unless bs.data_class.nil?
+          puts "top" if $DEBUG
+          self.topology = bs.topology unless bs.topology.nil?
+          puts "datec" if $DEBUG
+          self.date_created = bs.date_created unless bs.date_created.nil?
+          puts "datemod" if $DEBUG
+          self.date_modified = bs.date_modified unless bs.date_modified.nil?
+          puts "key" if $DEBUG
+
+          bs.keywords.each do |kw|
+            #write as qualifier every secondary accessions into the array
+            self.keywords = kw
+          end unless bs.keywords.nil?
+
+          puts "spec" if $DEBUG
+          #self.species = bs.species unless bs.species.nil?
+          self.species = bs.species unless bs.species.empty?
+          puts "Debug: #{bs.species}" if $DEBUG
+          puts "Debug: feat..start" if $DEBUG
+
+          bs.features.each do |feat|
+            self.feature=feat
+          end unless bs.features.nil?
+
+          puts "Debug: feat...end" if $DEBUG
+          bs.references.each do |reference|
+            self.reference=reference
+          end unless bs.references.nil?
+
+          bs.comments.each do |comment|
+            self.comment=comment
+          end unless bs.comments.nil?
+
+          #DELETE          end #transaction
+          return self
+        rescue Exception => e
+          puts "to_biosql exception: #{e}"
+          puts $!
+        end #rescue
+      end #to_biosql
+
+
+      def name
+        @entry.name
+      end
+      alias entry_id name
+
+      def name=(value)
+        @entry.name=value
+      end
+      alias entry_id= name=
+
+      def primary_accession
+        @entry.accession
+      end
+
+      def primary_accession=(value)
+        @entry.accession=value
+      end
+
+      #TODO      def secondary_accession
+      #        @entry.bioentry_qualifier_values
+      #      end
+
+      def organism
+        @entry.taxon.nil? ? "" : "#{@entry.taxon.taxon_scientific_name.name}"+ (@entry.taxon.taxon_genbank_common_name ? "(#{@entry.taxon.taxon_genbank_common_name.name})" : '')
+      end
+      alias species organism
+
+      def organism=(value)
+        #FIX there is a shortcut
+        taxon_name=TaxonName.first(:conditions=>["name = ? and name_class = ?",value.gsub(/\s+\(.+\)/,''),'scientific name'])
+        if taxon_name.nil?
+          puts "Error value doesn't exists in taxon_name table with scientific name constraint."
+        else
+          @entry.taxon_id=taxon_name.taxon_id
+          @entry.save
+        end
+      end
+      alias species= organism=
+
+      def database
+        @entry.biodatabase.name
+      end
+
+      def database_desc
+        @entry.biodatabase.description
+      end
+
+      def version
+        @entry.version
+      end
+      alias sequence_version version
+
+      def version=(value)
+        @entry.version=value
+      end
+      alias sequence_version= version=
+
+      def division
+        @entry.division
+      end
+
+      def division=(value)
+        @entry.division=value
+      end
+
+      def description
+        @entry.description
+      end
+      alias definition description
+
+      def description=(value)
+        @entry.description=value
+      end
+      alias definition= description=
+
+      def identifier
+        @entry.identifier
+      end
+      alias other_seqids identifier
+
+      def identifier=(value)
+        @entry.identifier=value
+      end
+
+      bioentry_qualifier_anchor :data_class
+      bioentry_qualifier_anchor :molecule_type, :synonym=>'mol_type'
+      bioentry_qualifier_anchor :topology
+      bioentry_qualifier_anchor :date_created
+      bioentry_qualifier_anchor :date_modified, :synonym=>'date_changed'
+      bioentry_qualifier_anchor :keywords, :synonym=>'keyword'
+      bioentry_qualifier_anchor :secondary_accessions, :synonym=>'secondary_accession'
+
+      def features
+        @entry.seqfeatures.collect do |sf|
+          self.get_seqfeature(sf)
+        end
+      end
+
+      def feature=(feat)
+        #ToDo: avoid Ontology find here, probably more efficient create class variables
+        #DELETE        type_term_ontology = Ontology.find_or_create({:name=>'SeqFeature Keys'})
+        puts "feature:type_term = #{feat.feature}" if $DEBUG
+        type_term = Term.first(:conditions=>["name = ?", feat.feature]) || Term.create({:name=>feat.feature, :ontology=>Ontology.first(:conditions=>["name = ?",'SeqFeature Keys'])})
+        #DELETE        source_term_ontology = Ontology.find_or_create({:name=>'SeqFeature Sources'})
+        puts "feature:source_term" if $DEBUG
+        source_term = Term.first(:conditions=>["name = ?",'EMBLGenBankSwit'])
+        puts "feature:seqfeature" if $DEBUG
+        seqfeature = @entry.seqfeatures.build({:source_term=>source_term, :type_term=>type_term, :rank=>@entry.seqfeatures.count.succ, :display_name=>''})
+        seqfeature.save
+        puts "feature:location" if $DEBUG
+        feat.locations.each do |loc|
+          location = seqfeature.locations.build({:seqfeature=>seqfeature, :start_pos=>loc.from, :end_pos=>loc.to, :strand=>loc.strand, :rank=>seqfeature.locations.count.succ})
+          location.save
+        end
+
+        #DELETE        qual_term_ontology = Ontology.find_or_create({:name=>'Annotation Tags'})
+
+        puts "feature:qualifier" if $DEBUG
+        feat.each do |qualifier|
+          #DELETE          qual_term = Term.find_or_create({:name=>qualifier.qualifier}, {:ontology=>qual_term_ontology})
+          qual_term = Term.first(:conditions=>["name = ?", qualifier.qualifier]) || Term.create({:name=>qualifier.qualifier, :ontology=>Ontology.first(:conditions=>["name = ?", 'Annotation Tags'])})
+          qual = seqfeature.seqfeature_qualifier_values.build({:seqfeature=>seqfeature, :term=>qual_term, :value=>qualifier.value.to_s, :rank=>seqfeature.seqfeature_qualifier_values.count.succ})
+          qual.save
+
+        end
+      end
+
+      #return the seqfeature mapped from BioSQL with a type_term like 'CDS'
+      def cdsfeatures
+        @entry.cdsfeatures
+      end
+
+      # Returns the sequence.
+      # Returns a Bio::Sequence::Generic object.
+
+      def seq
+        s = @entry.biosequence
+        Bio::Sequence::Generic.new(s ? s.seq : '')
+      end
+
+      def seq=(value)
+        #TODO: revise this piece of code.
+        #chk which type of alphabet is, NU/NA/nil
+        if @entry.biosequence.nil?
+          #DELETE          puts "intoseq1"
+          @entry.biosequence = Biosequence.new(:seq=>value)
+          #          biosequence = @entry.biosequence.build({:seq=>value})
+          @entry.biosequence.save
+          #          biosequence.save
+        else
+          @entry.biosequence.seq=value
+        end
+        self.length=value.length
+        #DELETE        #@entry.biosequence.length=value.length
+        #DELETE        #break
+        @entry.save
+      end
+
+      #report parents and exclude info with "no rank". Now I report rank == class but ... Question ? Have to be reported taxonomy with rank=="class"?
+      def taxonomy
+        tax = []
+        taxon = Taxon.first(:conditions=>["taxon_id = ?",@entry.taxon.parent_taxon_id])
+        while taxon and taxon.taxon_id != taxon.parent_taxon_id and taxon.node_rank!='no rank'
+          tax << taxon.taxon_scientific_name.name if taxon.node_rank!='class'
+          #Note: I don't like this call very much, correct with a relationship in the ref class.
+          taxon = Taxon.first(:conditions=>["taxon_id = ?",taxon.parent_taxon_id])
+        end
+        tax.reverse
+      end
+
+      def length
+        @entry.biosequence.length
+      end
+
+      def references
+        #return and array of hash, hash has these keys ["title", "dbxref_id", "reference_id", "authors", "crc", "location"]
+        #probably would be better to d a class refrence to collect these informations
+        @entry.bioentry_references.collect do |bio_ref|
+          hash = Hash.new
+          hash['authors'] = bio_ref.reference.authors.gsub(/\.\s/, "\.\s\|").split(/\|/) if (bio_ref.reference and bio_ref.reference.authors)
+
+          hash['sequence_position'] = "#{bio_ref.start_pos}-#{bio_ref.end_pos}" if (bio_ref.start_pos and bio_ref.end_pos)
+          hash['title'] = bio_ref.reference.title
+          hash['embl_gb_record_number'] = bio_ref.rank
+          #TODO: solve the problem with specific comment per reference.
+          #TODO: get dbxref
+          #take a look when location is build up in def reference=(value)
+
+          bio_ref.reference.location.split('|').each do |element|
+            key,value=element.split('=')
+            hash[key]=value
+          end unless bio_ref.reference.location.nil?
+
+          hash['xrefs'] = bio_ref.reference.dbxref ? "#{bio_ref.reference.dbxref.dbname}; #{bio_ref.reference.dbxref.accession}." : ''
+          Bio::Reference.new(hash)
+        end
+      end
+
+      def comments
+        @entry.comments.map do |comment|
+          comment.comment_text
+        end
+      end
+
+      def reference=(value)       
+        locations=Array.new
+        locations << "journal=#{value.journal}" unless value.journal.empty?
+        locations << "volume=#{value.volume}" unless value.volume.empty?
+        locations << "issue=#{value.issue}" unless value.issue.empty?
+        locations << "pages=#{value.pages}" unless value.pages.empty?
+        locations << "year=#{value.year}" unless value.year.empty?
+        locations << "pubmed=#{value.pubmed}" unless value.pubmed.empty?
+        locations << "medline=#{value.medline}" unless value.medline.empty?
+        locations << "doi=#{value.doi}" unless value.doi.nil?
+        locations << "abstract=#{value.abstract}" unless value.abstract.empty?
+        locations << "url=#{value.url}" unless value.url.nil?
+        locations << "mesh=#{value.mesh}" unless value.mesh.empty?
+        locations << "affiliations=#{value.affiliations}" unless value.affiliations.empty?
+        locations << "comments=#{value.comments.join('~')}"unless value.comments.nil?
+        start_pos, end_pos = value.sequence_position ? value.sequence_position.gsub(/\s*/,'').split('-') : [nil,nil]
+        reference= Reference.first(:conditions=>["title = ?",value.title]) || Reference.create({:title=>value.title,:authors=>value.authors.join(' '), :location=>locations.join('|')})
+        bio_reference=@entry.bioentry_references.build({:reference=>reference,:rank=>value.embl_gb_record_number, :start_pos=>start_pos, :end_pos=>end_pos})
+        bio_reference.save
+      end
+
+      def comment=(value)
+        #DELETE        comment=Comment.new({:bioentry=>@entry, :comment_text=>value, :rank=>@entry.comments.count.succ})
+        comment = @entry.comments.build({:comment_text=>value, :rank=>@entry.comments.count.succ})
+        comment.save
+      end
+
+      def save
+        #I should add chks for SQL errors
+        @entry.biosequence.save
+        @entry.save
+      end
+      def to_fasta
+        ">" + accession + "\n" + seq.gsub(Regexp.new(".{1,#{60}}"), "\\0\n")
+      end
+
+      def to_fasta_reverse_complememt
+        ">" + accession + "\n" + seq.reverse_complement.gsub(Regexp.new(".{1,#{60}}"), "\\0\n")
+      end
+
+      def to_biosequence
+        Bio::Sequence.adapter(self,Bio::Sequence::Adapter::BioSQL)
+      end
+    end #Sequence
+  end #SQL
+end #Bio